Duffyella gerundensis (LMG 28990, CCOS 903, EM595)

Name: Duffyella gerundensis (LMG 28990, CCOS 903, EM595)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140886

Type strain

Strain Designation EM595

Culture col. no. LMG 28990 CCOS 903 EM595

NCBI tax ID(s) 1619313

Special Collections Literature strains

Links

Duffyella gerundensis EM595 is a facultative anaerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from La Tallada d'Empordà , from leaves of pear .

Gram-negative motile rod-shaped colony-forming facultative anaerobe 16S sequence Bacteria

Name and taxonomic classification

SI-ID 396431

LMG 28990,CFBP 8471

@ref 20215

Last LPSN update 2026-02-09 11:33:44

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Enterobacterales

Family Erwiniaceae

Genus Duffyella

Species Duffyella gerundensis

Full scientific name Duffyella gerundensis (Rezzonico et al. 2016) Soutar and Stavrinides 2023

Synonyms (1)

Erwinia gerundensis

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
43715	negative	1-3 µm	0.5-1.3 µm	rod-shaped

Colony morphology

@ref	Colony color	Colony shape	Medium used
43715	Yellow	circular	Nutrient Agar

Culture and growth conditions

Culture medium

@ref	Name	Growth
43715	Nutrient agar (NA)

Physiology and metabolism

Oxygen tolerance

43715

Oxygen tolerancefacultative anaerobe

Spore formation

43715

Spore formationno

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43715	27613 ChEBI	amygdalin	-	assimilation
43715	18305 ChEBI	arbutin	+	builds acid from
43715	17108 ChEBI	D-arabinose	-	assimilation
43715	18333 ChEBI	D-arabitol	-	assimilation
43715	18333 ChEBI	D-arabitol	-	fermentation
43715	15824 ChEBI	D-fructose	+	builds acid from
43715	28847 ChEBI	D-fucose	-	assimilation
43715	12936 ChEBI	D-galactose	+	builds acid from
43715	17634 ChEBI	D-glucose	+	builds acid from
43715	62318 ChEBI	D-lyxose	-	assimilation
43715	16899 ChEBI	D-mannitol	+	builds acid from
43715	16899 ChEBI	D-mannitol	+	fermentation
43715	16024 ChEBI	D-mannose	+	fermentation
43715	16988 ChEBI	D-ribose	+	builds acid from
43715	16443 ChEBI	D-tagatose	-	assimilation
43715	65327 ChEBI	D-xylose	+	builds acid from
43715	17113 ChEBI	erythritol	-	assimilation
43715	16813 ChEBI	galactitol	-	assimilation
43715	28066 ChEBI	gentiobiose	-	assimilation
43715	17754 ChEBI	glycerol	+	builds acid from
43715	17754 ChEBI	glycerol	+	fermentation
43715	28087 ChEBI	glycogen	-	assimilation
43715	15443 ChEBI	inulin	-	assimilation
43715	30849 ChEBI	L-arabinose	+	builds acid from
43715	30849 ChEBI	L-arabinose	+	fermentation
43715	18403 ChEBI	L-arabitol	-	assimilation
43715	18287 ChEBI	L-fucose	-	assimilation
43715	62345 ChEBI	L-rhamnose	+	builds acid from
43715	62345 ChEBI	L-rhamnose	+	fermentation
43715	17266 ChEBI	L-sorbose	-	assimilation
43715	65328 ChEBI	L-xylose	-	assimilation
43715	17716 ChEBI	lactose	+	builds acid from
43715	17306 ChEBI	maltose	+	builds acid from
43715	17306 ChEBI	maltose	+	fermentation
43715	37684 ChEBI	mannose	+	builds acid from
43715	6731 ChEBI	melezitose	-	assimilation
43715	28053 ChEBI	melibiose	+	builds acid from
43715	28053 ChEBI	melibiose	+	fermentation
43715	320061 ChEBI	methyl alpha-D-glucopyranoside	-	assimilation
43715	43943 ChEBI	methyl alpha-D-mannoside	-	assimilation
43715	74863 ChEBI	methyl beta-D-xylopyranoside	-	assimilation
43715	17268 ChEBI	myo-inositol	+	builds acid from
43715	17268 ChEBI	myo-inositol	+	fermentation
43715	506227 ChEBI	N-acetylglucosamine	+	builds acid from
43715	17632 ChEBI	nitrate	+	reduction
43715		potassium 2-dehydro-D-gluconate	+	builds acid from
43715		potassium 2-dehydro-D-gluconate	+	fermentation
43715		potassium 5-dehydro-D-gluconate	-	assimilation
43715	32032 ChEBI	potassium gluconate	+	builds acid from
43715	32032 ChEBI	potassium gluconate	+	fermentation
43715	16634 ChEBI	raffinose	+	builds acid from
43715	16634 ChEBI	raffinose	+	fermentation
43715	15963 ChEBI	ribitol	-	assimilation
43715	28017 ChEBI	starch	-	assimilation
43715	17992 ChEBI	sucrose	+	builds acid from
43715	17992 ChEBI	sucrose	+	fermentation
43715	27082 ChEBI	trehalose	+	builds acid from
43715	32528 ChEBI	turanose	-	assimilation
43715	17151 ChEBI	xylitol	-	assimilation
43715	17151 ChEBI	xylitol	-	fermentation

Metabolite production

@ref	Chebi-ID	Metabolite
43715	15688 ChEBI	acetoin
43715	16136 ChEBI	hydrogen sulfide
43715	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
43715	catalase	+	1.11.1.6
43715	cytochrome oxidase	-	1.9.3.1
43715	urease	-	3.5.1.5

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	palmitate biosynthesis	100	22 of 22
66794	gluconeogenesis	100	8 of 8
66794	acetoin degradation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	coenzyme A metabolism	100	4 of 4
66794	enterobactin biosynthesis	100	3 of 3
66794	formaldehyde oxidation	100	3 of 3
66794	biotin biosynthesis	100	4 of 4
66794	glycogen metabolism	100	5 of 5
66794	acetate fermentation	100	4 of 4
66794	quinate degradation	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	threonine metabolism	100	10 of 10
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	aerobactin biosynthesis	100	1 of 1
66794	taurine degradation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	glutathione metabolism	92.86	13 of 14
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	pentose phosphate pathway	90.91	10 of 11
66794	metabolism of disaccharids	90.91	10 of 11
66794	starch degradation	90	9 of 10
66794	Entner Doudoroff pathway	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	heme metabolism	85.71	12 of 14
66794	vitamin B1 metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	vitamin B6 metabolism	81.82	9 of 11
66794	methionine metabolism	80.77	21 of 26
66794	peptidoglycan biosynthesis	80	12 of 15
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	allantoin degradation	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	purine metabolism	76.6	72 of 94
66794	lactate fermentation	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	oxidative phosphorylation	73.63	67 of 91
66794	flavin biosynthesis	73.33	11 of 15
66794	degradation of sugar acids	72	18 of 25
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	urea cycle	69.23	9 of 13
66794	alanine metabolism	68.97	20 of 29
66794	degradation of pentoses	67.86	19 of 28
66794	octane oxidation	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	degradation of hexoses	66.67	12 of 18
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	cyanate degradation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	non-pathway related	65.79	25 of 38
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	lipid metabolism	64.52	20 of 31
66794	pyrimidine metabolism	64.44	29 of 45
66794	arginine metabolism	62.5	15 of 24
66794	leucine metabolism	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	cellulose degradation	60	3 of 5
66794	myo-inositol biosynthesis	60	6 of 10
66794	lipoate biosynthesis	60	3 of 5
66794	methylglyoxal degradation	60	3 of 5
66794	histidine metabolism	58.62	17 of 29
66794	tryptophan metabolism	57.89	22 of 38
66794	propanol degradation	57.14	4 of 7
66794	citric acid cycle	57.14	8 of 14
66794	lysine metabolism	54.76	23 of 42
66794	proline metabolism	54.55	6 of 11
66794	ascorbate metabolism	50	11 of 22
66794	kanosamine biosynthesis II	50	1 of 2
66794	sphingosine metabolism	50	3 of 6
66794	ribulose monophosphate pathway	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	degradation of sugar alcohols	50	8 of 16
66794	tyrosine metabolism	50	7 of 14
66794	butanoate fermentation	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	CDP-diacylglycerol biosynthesis	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	ethanol fermentation	50	1 of 2
66794	3-phenylpropionate degradation	46.67	7 of 15
66794	sulfate reduction	46.15	6 of 13
66794	d-xylose degradation	45.45	5 of 11
66794	polyamine pathway	43.48	10 of 23
66794	carotenoid biosynthesis	40.91	9 of 22
66794	vitamin K metabolism	40	2 of 5
66794	gallate degradation	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	carnitine metabolism	37.5	3 of 8
66794	IAA biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	sulfoquinovose degradation	33.33	1 of 3
66794	1,4-dihydroxy-6-naphthoate biosynthesis	33.33	2 of 6
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	coenzyme M biosynthesis	30	3 of 10
66794	phenol degradation	30	6 of 20
66794	propionate fermentation	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	toluene degradation	25	1 of 4
66794	androgen and estrogen metabolism	25	4 of 16
66794	nitrate assimilation	22.22	2 of 9
66794	daunorubicin biosynthesis	22.22	2 of 9

Fatty acid profile

Metadata FA analysis

@ref

43715

Fatty acid	Percentage
C15:0 anteiso	24.5
C15:0 iso	21.1
C13:0 anteiso	8.3
C14:0 iso	7.2
C13:0 iso	6.4
C14:0	6.3
C15:0 iso 3OH	3.7
C16:0 3OH	3
C15:0	2.5
C17:0 iso 3OH	2.1
C12:0 iso	2
C16:0 iso 3OH	1.9
C11:0 anteiso	1.9
C16:0	1.7
C15:0 3OH	1.3
C16:1ω7c / C15:0 iso 2OH	0.7
C17:0 2OH	0.6

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Leaf (Phyllosphere)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
43715	La Tallada d'Empordà (Girona), from leaves of pear (Pyrus communis)	Girona	Spain	ESP	Europe

Interaction and safety

Sequence information

16S sequences

@ref	Description	Accession	Database
43715	Duffyella gerundensis strain EM595 16S ribosomal RNA gene, partial sequence	FJ611848

GC content

@ref	GC-content (mol%)	Method
43715	54.5	high performance liquid chromatography (HPLC)

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Erwinia gerundensis sp. nov., a cosmopolitan epiphyte originally isolated from pome fruit trees.	Rezzonico F, Smits THM, Born Y, Blom J, Frey JE, Goesmann A, Cleenwerck I, de Vos P, Bonaterra A, Duffy B, Montesinos E	Int J Syst Evol Microbiol	10.1099/ijsem.0.000920	2016

References

#20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#43715	Fabio Rezzonico, Theo H. M. Smits, Yannick Born, Jochen Blom, Jürg E. Frey, Alexander Goesmann, Ilse Cleenwerck, Paul de Vos, Anna Bonaterra, Brion Duffy, Emilio Montesinos: Erwinia gerundensis sp. nov., a cosmopolitan epiphyte originally isolated from pome fruit trees. IJSEM 66: 1583 - 1592 2016 ( DOI 10.1099/ijsem.0.000920 , PubMed 26813696 )
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Duffyella gerundensis (LMG 28990, CCOS 903, EM595)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Enzymes

Pathway annotation

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Sequence information

16S sequences

GC content

Genome-based predictions

Literature

Literature

References

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